Service theft deterrent system turned on after the battery drained?

Here is how to reset the system:

Disarming an Armed System/Silencing an Alarm
If system arming has been requested by the power door lock switch or the keyless entry transmitter, it must be disarmed.

Note: Disconnecting the battery or removing fuses does not disable the arm or alarm modes, since the BCM stores the content theft deterrent mode status in memory.
To disarm the content theft deterrent system in standby mode, perform one of the following:
Press the UNLOCK button on the keyless entry transmitter.
Approach the vehicle with a valid keyless entry transmitter and pull the vehicle door handle (RPO ATH).
Insert a valid key into the ignition and switch to the ON position.
To disarm the content theft deterrent system in the armed mode (non-event) or when activated (during an alarm event):
Press the UNLOCK button on the keyless entry transmitter.
Insert a valid key into the ignition and switch to the ON position

There is a warning and a specific procedure to replace the battery. You might want to try disconnecting the battery overnight if the reset does not work.

Warning: Unless directed otherwise, the ignition must be OFF with the key removed, and all electrical loads must be Off before servicing any electrical component. Disconnect the negative battery cable to prevent an electrical spark should a tool or equipment come in contact with an exposed electrical terminal. Failure to follow these precautions may result in personal injury and/or damage to the vehicle or its components.

For Vehicles equipped with OnStar (UE1) with Back Up Battery:

The Back Up Battery is a redundant power supply to allow limited OnStar functionality in the event of a main vehicle battery power disruption to the VCIM (OnStar module). Do not disconnect the main vehicle battery or remove the OnStar fuse with the ignition key in any position other than OFF. Retained accessory power should be allowed to time out or be disabled (simply opening the driver door should disable retained accessory power) before disconnecting power. Disconnecting power to the OnStar module in any way while the ignition is On or with retained accessory power activated may cause activation of the OnStar Back-Up Battery system and will discharge and permanently damage the back-up battery. Once the Back-Up Battery is activated it will stay on until it has completely discharged. The back-up battery is not rechargeable and once activated the back-up battery must be replaced.

Check out the images (below). Please let us know what happens.

It sounds like you had a voltage surge when you connected the battery which may have taken out the BCM, we should do a CAN scan to see what codes are stored. You can get a CAN scanner (Controller Area Network) which will work on most cars from Amazon.

Here is a video to show you how:

https://youtu.be/u-4syLc-ifQ

and

https://www.2carpros.com/articles/can-scan-controller-area-network-easy

Please go over this guide and get back to us.

Anything?